LAMMPS (27 May 2021)
# Run NPT MD simulation for Si at 500 K.
variable nsteps index 100 #0

# NOTE: These are not intended to represent real materials

units           metal

atom_style      atomic
atom_modify     map array
boundary        p p p
atom_modify     sort 0 0.0

#read_data Si.data
lattice         diamond 5.43
Lattice spacing in x,y,z = 5.4300000 5.4300000 5.4300000
region          box block 0 2 0 2 0 2
create_box      1 box
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.860000 10.860000 10.860000)
  1 by 1 by 1 MPI processor grid
create_atoms    1 box
Created 64 atoms
  create_atoms CPU = 0.000 seconds
mass            1 29.0

# temperature
variable t equal 500.


# Potential
#pair_style mliap model nn Si-snap/NN_weights.txt descriptor sna Si-snap/DescriptorParam.txt
pair_style mliap model nn Si.nn.mliap.model descriptor so3 Si.nn.mliap.descriptor
SO3 keyword rcutfac 5.0 
SO3 keyword nmax 3 
SO3 keyword lmax 4 
SO3 keyword alpha 2.0 
SO3 keyword nelems 1 
SO3 keyword elems Si 
SO3 keyword radelems 0.5 
SO3 keyword welems 14 
pair_coeff * * Si Si

# Set-up output

compute  eatom all pe/atom
compute  energy all reduce sum c_eatom

compute  satom all stress/atom NULL
compute  str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)

thermo_style    custom step temp epair c_energy etotal press v_press
thermo          10
thermo_modify norm yes

# Set up NVE run

timestep 0.5e-3
neighbor 1.0 bin
neigh_modify once no every 1 delay 0 check yes

# Run MD

velocity all create $t 5287287 loop geom
velocity all create 500 5287287 loop geom
fix 1 all npt temp ${t} ${t} 0.2 iso 0.0 0.0 2
fix 1 all npt temp 500 ${t} 0.2 iso 0.0 0.0 2
fix 1 all npt temp 500 500 0.2 iso 0.0 0.0 2
run ${nsteps}
run 100
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 6
  ghost atom cutoff = 6
  binsize = 3, bins = 4 4 4
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair mliap, perpetual
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 298.3 | 298.3 | 298.3 Mbytes
Step Temp E_pair c_energy TotEng Press v_press 
       0          500   -3.8376374   -3.8376374   -3.7740172   -7295.2456    7295.2456 
      10       489.81   -3.8363423   -3.8363423   -3.7740187   -6964.5624    6964.5624 
      20    460.24523   -3.8325828   -3.8325828    -3.774021   -6014.7165    6014.7165 
      30     414.4367    -3.826752    -3.826752   -3.7740189   -4572.0641    4572.0641 
      40    358.34511   -3.8196022   -3.8196022   -3.7740062   -2849.9177    2849.9177 
      50    300.80447   -3.8122536   -3.8122536   -3.7739791   -1128.7008    1128.7008 
      60     251.6276   -3.8059543   -3.8059543   -3.7739371    306.20639   -306.20639 
      70    218.02888   -3.8016236   -3.8016236   -3.7738815    1253.4391   -1253.4391 
      80    201.70095   -3.7994767   -3.7994767   -3.7738122    1661.6675   -1661.6675 
      90    198.91416   -3.7990366   -3.7990366   -3.7737266      1628.78     -1628.78 
     100    203.36197    -3.799497    -3.799497   -3.7736212    1338.0458   -1338.0458 
Loop time of 3.39264 on 1 procs for 100 steps with 64 atoms

Performance: 1.273 ns/day, 18.848 hours/ns, 29.476 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.391      | 3.391      | 3.391      |   0.0 | 99.95
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0.00029302 | 0.00029302 | 0.00029302 |   0.0 |  0.01
Output  | 0.00039387 | 0.00039387 | 0.00039387 |   0.0 |  0.01
Modify  | 0.00074792 | 0.00074792 | 0.00074792 |   0.0 |  0.02
Other   |            | 0.0002153  |            |       |  0.01

Nlocal:        64.0000 ave          64 max          64 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        557.000 ave         557 max         557 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         0.00000 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:      2944.00 ave        2944 max        2944 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 2944
Ave neighs/atom = 46.000000
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03
